US9006242B2 - Substituted benzene compounds - Google Patents

Substituted benzene compounds Download PDF

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US9006242B2
US9006242B2 US14/054,695 US201314054695A US9006242B2 US 9006242 B2 US9006242 B2 US 9006242B2 US 201314054695 A US201314054695 A US 201314054695A US 9006242 B2 US9006242 B2 US 9006242B2
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methyl
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amino
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US20140107122A1 (en
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Kevin Wayne Kuntz
John Emmerson CAMPBELL
Masashi Seki
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Eisai R&D Management Co Ltd
Epizyme Inc
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Epizyme Inc
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Priority to US15/359,538 priority patent/US10098888B2/en
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4412—Non condensed pyridines; Hydrogenated derivatives thereof having oxo groups directly attached to the heterocyclic ring
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4427—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems
    • A61K31/444—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems containing a six-membered ring with nitrogen as a ring heteroatom, e.g. amrinone
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445—Non condensed piperidines, e.g. piperocaine
    • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
    • A61K31/4545—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a six-membered ring with nitrogen as a ring hetero atom, e.g. pipamperone, anabasine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D213/00—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members
    • C07D213/02—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
    • C07D213/04—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D213/24—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D213/44—Radicals substituted by doubly-bound oxygen, sulfur, or nitrogen atoms, or by two such atoms singly-bound to the same carbon atom
    • C07D213/46—Oxygen atoms
    • C07D213/50—Ketonic radicals
    • C—CHEMISTRY; METALLURGY
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    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D213/00—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members
    • C07D213/02—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
    • C07D213/04—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D213/60—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D213/62—Oxygen or sulfur atoms
    • C07D213/63—One oxygen atom
    • C07D213/64—One oxygen atom attached in position 2 or 6
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/02—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings
    • C07D405/12—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/14—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
    • C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
    • C07D413/12—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
    • C07D413/14—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing three or more hetero rings

Definitions

  • the present invention features a substituted benzene compound selected from
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the present invention also provides pharmaceutical compositions comprising one or more pharmaceutically acceptable carriers and one or more compounds disclosed herein.
  • Another aspect of this invention is a method of treating or preventing an EZH2-mediated disorder.
  • the method includes administering to a subject in need thereof a therapeutically effective amount of one or more compounds disclosed herein.
  • the EZH2-mediated disorder is a disease, disorder, or condition that is mediated at least in part by the activity of EZH2.
  • the EZH2-mediated disorder is related to an increased EZH2 activity.
  • the EZH2-mediated disorder is a cancer.
  • the EZH2-mediated cancer may be lymphoma, leukemia or melanoma, for example, diffuse large B-cell lymphoma (DLBCL), non-Hodgkin's lymphoma (NHL), follicular lymphoma, chronic myelogenous leukemia (CML), acute myeloid leukemia, acute lymphocytic leukemia, mixed lineage leukemia, or myelodysplastic syndromes (MDS).
  • the EZH2-mediated cancer may be a malignant rhabdoid tumor or INI1-defecient tumor.
  • malignant rhabdoid tumor The histologic diagnosis of malignant rhabdoid tumor depends on identification of characteristic rhabdoid cells (large cells with eccentrically located nuclei and abundant, eosinophilic cytoplasm) and immunohistochemistry with antibodies to vimentin, keratin and epithelial membrane antigen.
  • the SMARCB1/INI1 gene located in chromosome band 22q11.2, is inactivated by deletions and/or mutations.
  • the malignant rhabdoid tumors may be INI1-defecient tumor.
  • any description of a method of treatment includes uses of the compounds to provide such treatment or prophylaxis as is described in the specification, as well as uses of the compounds to prepare a medicament to treat or prevent such condition.
  • the treatment includes treatment of human or non-human animals including rodents and other disease models.
  • the compounds or methods described herein may be used for research (e.g., studying epigenetic enzymes) and other non-therapeutic purposes.
  • the preferred compounds disclosed herein have desirable pharmacological and/or pharmacokinetic properties, e.g., low clearance rates and/or limited risk of adverse drug-drug interactions in combination therapy evaluated, for example, through time-dependent and reversible inhibition of cytochrome P-450 enzymes.
  • FIG. 3 is a diagram showing concentration of Compound 1 in tumor at day 7 or day 28 post treatment or concentration of Compound A in tumor at day 7 post treatment.
  • A though “G” denote 7 days post administration of Compound 1 at dosages of 62.5, 83.3, 125, 166.7, 250, 333.3, and 500 mg/kg, respectively;
  • H and “I” denote 7 days post administration of Compound A at dosages of 125 and 250 mg/kg, respectively;
  • “J” through “L” denote 28 days post administration of Compound 1 at dosages of 62.5, 125 and 250 mg/kg, respectively.
  • FIG. 4 is a diagram showing concentration of Compound 1 or Compound A in plasma at day 7 or day 28 post treatment.
  • the top dashed line indicates the plasma protein binding (PPB) corrected LCC of Compound A and the bottom dashed line indicates PPB corrected LCC of Compound 1.
  • PPB plasma protein binding
  • FIG. 5 is a diagram showing global H3K27me3 methylation in KARPAS-422 tumors from mice treated with Compound 1 or Compound A for 7 days.
  • A denotes vehicle treatment
  • B though “H” denote treatment with Compound 1 at dosages of 62.5, 83.3, 125, 166.7, 250, 333.3, and 500 mg/kg, respectively
  • I and “J” denote treatment with Compound A at dosages of 125 and 250 mg/kg, respectively.
  • FIG. 6 is a diagram showing global H3K27me3 methylation in KARPAS-422 tumors from mice treated with Compound 1 for 28 days.
  • FIG. 7 is a diagram showing global H3K27me3 methylation in bone marrow from KARPAS-422 xenograft tumor bearing mice treated with Compound 1 or Compound A for 7 days.
  • A denotes vehicle treatment
  • B though “H” denote treatment with Compound 1 at dosages of 62.5, 83.3, 125, 166.7, 250, 333.3, and 500 mg/kg, respectively
  • I and J denote treatment with Compound A at dosages of 125 and 250 mg/kg, respectively.
  • FIG. 8 is a diagram showing global H3K27me3 methylation in bone marrow from KARPAS-422 xenograft tumor bearing mice treated with Compound 1 for 28 days.
  • A denotes vehicle treatment
  • B though “E” denote treatment with Compound 1 at dosages of 62.5, 125, 250, and 500 mg/kg, respectively
  • F denotes treatment with Compound A at a dosage of 250 mg/kg.
  • the present invention provides novel substituted benzene compounds, synthetic methods for making the compounds, pharmaceutical compositions containing them and various uses of the compounds.
  • Representative compounds of the present invention include compounds listed in Table 1.
  • the structural formula of the compound represents a certain isomer for convenience in some cases, but the present invention may include all isomers, such as geometrical isomers, optical isomers based on an asymmetrical carbon, stereoisomers, tautomers, enantiomers, rotamers, diastereomers, racemates and the like, it being understood that not all isomers may have the same level of activity.
  • a crystal polymorphism may be present for the compounds represented by the formula. It is noted that any crystal form, crystal form mixture, or anhydride or hydrate thereof is included in the scope of the present invention.
  • “Isomerism” means compounds that have identical molecular formulae but differ in the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.” Stereoisomers that are not mirror images of one another are termed “diastereoisomers,” and stereoisomers that are non-superimposable mirror images of each other are termed “enantiomers” or sometimes optical isomers. A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a “racemic mixture.”
  • “Geometric isomer” means the diastereomers that owe their existence to hindered rotation about double bonds or a cycloalkyl linker (e.g., 1,3-cylcobutyl). These configurations are differentiated in their names by the prefixes cis and trans, or Z and E, which indicate that the groups are on the same or opposite side of the double bond in the molecule according to the Cahn-Ingold-Prelog rules.
  • atropic isomers are a type of stereoisomer in which the atoms of two isomers are arranged differently in space. Atropic isomers owe their existence to a restricted rotation caused by hindrance of rotation of large groups about a central bond. Such atropic isomers typically exist as a mixture, however as a result of recent advances in chromatography techniques, it has been possible to separate mixtures of two atropic isomers in select cases.
  • Tautomer is one of two or more structural isomers that exist in equilibrium and is readily converted from one isomeric form to another. This conversion results in the formal migration of a hydrogen atom accompanied by a switch of adjacent conjugated double bonds. Tautomers exist as a mixture of a tautomeric set in solution. In solutions where tautomerization is possible, a chemical equilibrium of the tautomers will be reached. The exact ratio of the tautomers depends on several factors, including temperature, solvent and pH. The concept of tautomers that are interconvertable by tautomerizations is called tautomerism.
  • keto-enol tautomerism a simultaneous shift of electrons and a hydrogen atom occurs.
  • Ring-chain tautomerism arises as a result of the aldehyde group (—CHO) in a sugar chain molecule reacting with one of the hydroxy groups (—OH) in the same molecule to give it a cyclic (ring-shaped) form as exhibited by glucose.
  • keto-enol equilibria is between pyridin-2(1H)-ones and the corresponding pyridin-2-ols, as shown below.
  • crystal polymorphs means crystal structures in which a compound (or a salt or solvate thereof) can crystallize in different crystal packing arrangements, all of which have the same elemental composition. Different crystal forms usually have different X-ray diffraction patterns, infrared spectral, melting points, density hardness, crystal shape, optical and electrical properties, stability and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Crystal polymorphs of the compounds can be prepared by crystallization under different conditions.
  • the compounds of this invention include the compounds themselves, such as any of the formulae disclosed herein.
  • the compounds of this invention may also include their salts, and their solvates, if applicable.
  • a salt for example, can be formed between an anion and a positively charged group (e.g., amino) on a substituted benzene compound.
  • Suitable anions include chloride, bromide, iodide, sulfate, bisulfate, sulfamate, nitrate, phosphate, citrate, methanesulfonate, trifluoroacetate, glutamate, glucuronate, glutarate, malate, maleate, succinate, fumarate, tartrate, tosylate, salicylate, lactate, naphthalenesulfonate, and acetate (e.g., trifluoroacetate).
  • pharmaceutically acceptable anion refers to an anion suitable for forming a pharmaceutically acceptable salt.
  • a salt can also be formed between a cation and a negatively charged group (e.g., carboxylate) on a substituted benzene compound.
  • Suitable cations include sodium ion, potassium ion, magnesium ion, calcium ion, and an ammonium cation such as tetramethylammonium ion.
  • the substituted benzene compounds also include those salts containing quaternary nitrogen atoms.
  • the compounds of the present invention can exist in either hydrated or unhydrated (the anhydrous) form or as solvates with other solvent molecules.
  • hydrates include monohydrates, dihydrates, etc.
  • solvates include ethanol solvates, acetone solvates, etc.
  • Solvate means solvent addition forms that contain either stoichiometric or non stoichiometric amounts of solvent. Some compounds have a tendency to trap a fixed molar ratio of solvent molecules in the crystalline solid state, thus forming a solvate. If the solvent is water the solvate formed is a hydrate; and if the solvent is alcohol, the solvate formed is an alcoholate. Hydrates are formed by the combination of one or more molecules of water with one molecule of the substance in which the water retains its molecular state as H 2 O.
  • analog refers to a chemical compound that is structurally similar to another but differs slightly in composition (as in the replacement of one atom by an atom of a different element or in the presence of a particular functional group, or the replacement of one functional group by another functional group).
  • an analog is a compound that is similar or comparable in function and appearance, but not in structure or origin to the reference compound.
  • derivative refers to compounds that have a common core structure, and are substituted with various groups as described herein. For example, all of the compounds in Table 1 are substituted benzene compounds, and have a common core.
  • bioisostere refers to a compound resulting from the exchange of an atom or of a group of atoms with another, broadly similar, atom or group of atoms.
  • the objective of a bioisosteric replacement is to create a new compound with similar biological properties to the parent compound.
  • the bioisosteric replacement may be physicochemically or topologically based.
  • Examples of carboxylic acid bioisosteres include, but are not limited to, acyl sulfonimides, tetrazoles, sulfonates and phosphonates. See, e.g., Patani and LaVoie, Chem. Rev. 96, 3147-3176, 1996.
  • the present invention is intended to include all isotopes of atoms occurring in the present compounds.
  • Isotopes include those atoms having the same atomic number but different mass numbers.
  • isotopes of hydrogen include tritium and deuterium
  • isotopes of carbon include C-13 and C-14.
  • the present invention provides methods for the synthesis of the compounds disclosed herein.
  • the present invention also provides detailed methods for the synthesis of various disclosed compounds of the present invention according to the schemes as shown in the Examples.
  • compositions are described as having, including, or comprising specific components, it is contemplated that compositions also consist essentially of or consist of the recited components.
  • methods or processes are described as having, including, or comprising specific process steps, the processes also consist essentially of, or consist of, the recited processing steps.
  • order of steps or order for performing certain actions is immaterial so long as the invention remains operable.
  • two or more steps or actions can be conducted simultaneously.
  • the synthetic processes of the invention can tolerate a wide variety of functional groups, therefore various substituted starting materials can be used.
  • the processes generally provide the desired final compound at or near the end of the overall process, although it may be desirable in certain instances to further convert the compound to a pharmaceutically acceptable salt thereof.
  • protecting groups may require protection from the reaction conditions via the use of protecting groups.
  • Protecting groups may also be used to differentiate similar functional groups in molecules.
  • a list of protecting groups and how to introduce and remove these groups can be found in Greene, T. W., Wuts, P. G. M., Protective Groups in Organic Synthesis, 3 rd edition, John Wiley & Sons: New York, 1999.
  • Preferred protecting groups include, but are not limited to:
  • di-alkyl acetals such as dimethoxy acetal or diethyl acetyl.
  • Compounds of the present invention inhibit the histone methyltransferase activity of EZH2 or a mutant thereof and, accordingly, in one aspect of the invention, certain compounds disclosed herein are candidates for treating, or preventing certain conditions and diseases in which EZH2 plays a role.
  • the present invention provides methods for treating conditions and diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, wherein said methylation status is mediated at least in part by the activity of EZH2. Modulation of the methylation status of histones can in turn influence the level of expression of target genes activated by methylation, and/or target genes suppressed by methylation.
  • the method includes administering to a subject in need of such treatment, a therapeutically effective amount of a compound of the present invention, or a pharmaceutically acceptable salt, polymorph, solvate, or stereoisomeror thereof.
  • any description of a method of treatment includes uses of the compounds to provide such treatment or prophylaxis as is described in the specification, as well as uses of the compounds to prepare a medicament to treat or prevent such condition.
  • the treatment includes treatment of human or non-human animals including rodents and other disease models.
  • this invention relates to a method of modulating the activity of the EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono- through tri-methylation of lysine 27 on histone H3 (H3-K27) in a subject in need thereof.
  • the method comprises the step of administering to a subject having a cancer expressing a mutant EZH2 a therapeutically effective amount of a compound described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer.
  • the EZH2-mediated cancer is selected from the group consisting of follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) of germinal center B cell-like (GCB) subtype.
  • the cancer is lymphoma, leukemia or melanoma.
  • the lymphoma is non-Hodgkin's lymphoma (NHL), follicular lymphoma or diffuse large B-cell lymphoma.
  • the leukemia is chronic myelogenous leukemia (CML), acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
  • the EZH2-mediated precancerous condition is myelodysplastic syndromes (MDS, formerly known as preleukemia).
  • the EZH2-mediated cancer is a hematological cancer.
  • the compound(s) of the present invention inhibit the histone methyltransferase activity of EZH2 or a mutant thereof and, accordingly, the present invention also provides methods for treating conditions and diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, wherein said methylation status is mediated at least in part by the activity of EZH2.
  • certain compounds disclosed herein are candidates for treating, or preventing certain conditions and diseases. Modulation of the methylation status of histones can in turn influence the level of expression of target genes activated by methylation, and/or target genes suppressed by methylation.
  • the method includes administering to a subject in need of such treatment, a therapeutically effective amount of a compound of the present invention.
  • a “subject” is interchangeable with a “subject in need thereof”, both of which refer to a subject having a disorder in which EZH2-mediated protein methylation plays a part, or a subject having an increased risk of developing such disorder relative to the population at large.
  • a “subject” includes a mammal.
  • the mammal can be e.g., a human or appropriate non-human mammal, such as primate, mouse, rat, dog, cat, cow, horse, goat, camel, sheep or a pig.
  • the subject can also be a bird or fowl.
  • the mammal is a human.
  • a subject in need thereof can be one who has been previously diagnosed or identified as having cancer or a precancerous condition.
  • a subject in need thereof can also be one who has (e.g., is suffering from) cancer or a precancerous condition.
  • a subject in need thereof can be one who has an increased risk of developing such disorder relative to the population at large (i.e., a subject who is predisposed to developing such disorder relative to the population at large).
  • a subject in need thereof can have a precancerous condition.
  • a subject in need thereof can have refractory or resistant cancer (i.e., cancer that doesn't respond or hasn't yet responded to treatment). The subject may be resistant at start of treatment or may become resistant during treatment. In some embodiments, the subject in need thereof has cancer recurrence following remission on most recent therapy.
  • the subject in need thereof received and failed all known effective therapies for cancer treatment. In some embodiments, the subject in need thereof received at least one prior therapy.
  • the subject has cancer or a cancerous condition.
  • the cancer is lymphoma, leukemia, melanoma, or rhabdomyosarcoma.
  • the lymphoma is non-Hodgkin's lymphoma, follicular lymphoma or diffuse large B-cell lymphoma.
  • the leukemia is chronic myelogenous leukemia (CML).
  • CML chronic myelogenous leukemia
  • the precancerous condition is myelodysplastic syndromes (MDS, formerly known as preleukemia).
  • treating describes the management and care of a patient for the purpose of combating a disease, condition, or disorder and includes the administration of a compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, to alleviate the symptoms or complications of a disease, condition or disorder, or to eliminate the disease, condition or disorder.
  • the term “treat” can also include treatment of a cell in vitro or an animal model.
  • a compound of the present invention can or may also be used to prevent a relevant disease, condition or disorder, or used to identify suitable candidates for such purposes.
  • preventing,” “prevent,” or “protecting against” describes reducing or eliminating the onset of the symptoms or complications of such disease, condition or disorder.
  • Point mutations of the EZH2 gene at a single amino acid residue (e.g., Y641, A677, and A687) of EZH2 have been reported to be linked to lymphoma. More examples of EZH2 mutants and methods of detection of mutation and methods treatment of mutation-associated disorders are described in, e.g., U.S. Patent Application Publication No. US 20130040906, the entire content of which is incorporated herein by reference in its entirety.
  • “combination therapy” or “co-therapy” includes the administration of a compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, and at least a second agent as part of a specific treatment regimen intended to provide the beneficial effect from the co-action of these therapeutic agents.
  • the beneficial effect of the combination includes, but is not limited to, pharmacokinetic or pharmacodynamic co-action resulting from the combination of therapeutic agents.
  • the present invention also provides pharmaceutical compositions comprising a compound disclosed herein in combination with at least one pharmaceutically acceptable excipient or carrier.
  • a “pharmaceutical composition” is a formulation containing the compounds of the present invention in a form suitable for administration to a subject.
  • the pharmaceutical composition is in bulk or in unit dosage form.
  • the unit dosage form is any of a variety of forms, including, for example, a capsule, an IV bag, a tablet, a single pump on an aerosol inhaler or a vial.
  • the quantity of active ingredient (e.g., a formulation of the disclosed compound or salt, hydrate, solvate or isomer thereof) in a unit dose of composition is an effective amount and is varied according to the particular treatment involved.
  • active ingredient e.g., a formulation of the disclosed compound or salt, hydrate, solvate or isomer thereof
  • the dosage will also depend on the route of administration.
  • routes including oral, pulmonary, rectal, parenteral, transdermal, subcutaneous, intravenous, intramuscular, intraperitoneal, inhalational, buccal, sublingual, intrapleural, intrathecal, intranasal, and the like.
  • Dosage forms for the topical or transdermal administration of a compound of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants.
  • the active compound is mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that are required.
  • the phrase “pharmaceutically acceptable” refers to those compounds, anions, cations, materials, compositions, carriers, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • “Pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic and neither biologically nor otherwise undesirable, and includes excipient that is acceptable for veterinary use as well as human pharmaceutical use.
  • a “pharmaceutically acceptable excipient” as used in the specification and claims includes both one and more than one such excipient.
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), and transmucosal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfate; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates, and agents for the adjustment of tonicity such as sodium chloride or dextrose.
  • the pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • a compound or pharmaceutical composition of the invention can be administered to a subject in many of the well-known methods currently used for chemotherapeutic treatment.
  • a compound of the invention may be injected directly into tumors, injected into the blood stream or body cavities or taken orally or applied through the skin with patches.
  • the dose chosen should be sufficient to constitute effective treatment but not so high as to cause unacceptable side effects.
  • the state of the disease condition e.g., cancer, precancer, and the like
  • the health of the patient should preferably be closely monitored during and for a reasonable period after treatment.
  • therapeutically effective amount refers to an amount of a pharmaceutical agent to treat, ameliorate, or prevent an identified disease or condition, or to exhibit a detectable therapeutic or inhibitory effect.
  • the effect can be detected by any assay method known in the art.
  • the precise effective amount for a subject will depend upon the subject's body weight, size, and health; the nature and extent of the condition; and the therapeutic or combination of therapeutics selected for administration.
  • Therapeutically effective amounts for a given situation can be determined by routine experimentation that is within the skill and judgment of the clinician.
  • the disease or condition to be treated is cancer.
  • the disease or condition to be treated is a cell proliferative disorder.
  • the therapeutically effective amount can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models, usually rats, mice, rabbits, dogs, or pigs.
  • the animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
  • Therapeutic/prophylactic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED 50 (the dose therapeutically effective in 50% of the population) and LD 50 (the dose lethal to 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD 50 /ED 50 .
  • Pharmaceutical compositions that exhibit large therapeutic indices are preferred. The dosage may vary within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
  • Dosage and administration are adjusted to provide sufficient levels of the active agent(s) or to maintain the desired effect.
  • Factors which may be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy.
  • Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation.
  • compositions containing active compounds of the present invention may be manufactured in a manner that is generally known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • Pharmaceutical compositions may be formulated in a conventional manner using one or more pharmaceutically acceptable carriers comprising excipients and/or auxiliaries that facilitate processing of the active compounds into preparations that can be used pharmaceutically. Of course, the appropriate formulation is dependent upon the route of administration chosen.
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS).
  • the composition must be sterile and should be fluid to the extent that easy syringeability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as manitol and sorbitol, and sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible pharmaceutically acceptable carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition.
  • the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a binder such as microcrystalline cellulose, gum tragacanth or gelatin
  • an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch
  • a lubricant such as magnesium stearate or Sterotes
  • a glidant such as colloidal silicon dioxide
  • the compounds are delivered in the form of an aerosol spray from pressured container or dispenser, which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
  • a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • the active compounds can be prepared with pharmaceutically acceptable carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art.
  • the materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved.
  • the dosages of the pharmaceutical compositions used in accordance with the invention vary depending on the agent, the age, weight, and clinical condition of the recipient patient, and the experience and judgment of the clinician or practitioner administering the therapy, among other factors affecting the selected dosage.
  • the dose should be sufficient to result in slowing, and preferably regressing, the growth of the tumors and also preferably causing complete regression of the cancer.
  • Dosages can range from about 0.01 mg/kg per day to about 5000 mg/kg per day. In preferred aspects, dosages can range from about 1 mg/kg per day to about 1000 mg/kg per day.
  • the dose will be in the range of about 0.1 mg/day to about 50 g/day; about 0.1 mg/day to about 25 g/day; about 0.1 mg/day to about 10 g/day; about 0.1 mg to about 3 g/day; or about 0.1 mg to about 1 g/day, in single, divided, or continuous doses (which dose may be adjusted for the patient's weight in kg, body surface area in m 2 , and age in years).
  • An effective amount of a pharmaceutical agent is that which provides an objectively identifiable improvement as noted by the clinician or other qualified observer. For example, regression of a tumor in a patient may be measured with reference to the diameter of a tumor. Decrease in the diameter of a tumor indicates regression. Regression is also indicated by failure of tumors to reoccur after treatment has stopped.
  • the term “dosage effective manner” refers to amount of an active compound to produce the desired biological effect in a subject or cell.
  • compositions can be included in a container, pack, or dispenser together with instructions for administration.
  • pharmaceutically acceptable salts refer to derivatives of the compounds of the present invention wherein the parent compound is modified by making acid or base salts thereof.
  • pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines, alkali or organic salts of acidic residues such as carboxylic acids, and the like.
  • the pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent compound formed, for example, from non-toxic inorganic or organic acids.
  • such conventional non-toxic salts include, but are not limited to, those derived from inorganic and organic acids selected from 2-acetoxybenzoic, 2-hydroxyethane sulfonic, acetic, ascorbic, benzene sulfonic, benzoic, bicarbonic, carbonic, citric, edetic, ethane disulfonic, 1,2-ethane sulfonic, fumaric, glucoheptonic, gluconic, glutamic, glycolic, glycollyarsanilic, hexylresorcinic, hydrabamic, hydrobromic, hydrochloric, hydroiodic, hydroxymaleic, hydroxynaphthoic, isethionic, lactic, lactobionic, lauryl sulfonic, maleic, malic, mandelic, methane sulfonic, napsylic, nitric, oxalic, pamoic, pantothenic, phenylacetic, phosphoric,
  • salts include hexanoic acid, cyclopentane propionic acid, pyruvic acid, malonic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, 4-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, 4-toluenesulfonic acid, camphorsulfonic acid, 4-methylbicyclo-[2.2.2]-oct-2-ene-1-carboxylic acid, 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, muconic acid, and the like.
  • the present invention also encompasses salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base such as ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.
  • a metal ion e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion
  • an organic base such as ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.
  • the ratio of the compound to the cation or anion of the salt can be 1:1, or any ration other than 1:1, e.g., 3:1, 2:1, 1:2, or 1:3.
  • the compounds, or pharmaceutically acceptable salts thereof are administered orally, nasally, transdermally, pulmonary, inhalationally, buccally, sublingually, intraperintoneally, subcutaneously, intramuscularly, intravenously, rectally, intrapleurally, intrathecally and parenterally.
  • the compound is administered orally.
  • One skilled in the art will recognize the advantages of certain routes of administration.
  • the dosage regimen utilizing the compounds is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal and hepatic function of the patient; and the particular compound or salt thereof employed.
  • An ordinarily skilled physician or veterinarian can readily determine and prescribe the effective amount of the drug required to prevent, counter, or arrest the progress of the condition.
  • the compounds described herein, and the pharmaceutically acceptable salts thereof are used in pharmaceutical preparations in combination with a pharmaceutically acceptable carrier or diluent.
  • suitable pharmaceutically acceptable carriers include inert solid fillers or diluents and sterile aqueous or organic solutions.
  • the compounds will be present in such pharmaceutical compositions in amounts sufficient to provide the desired dosage amount in the range described herein.
  • compounds may be drawn with one particular configuration (e.g., with or without a particular stereoisomer indicated) for simplicity.
  • Such particular configurations or lack thereof are not to be construed as limiting the invention to one or another isomer, tautomer, regioisomer or stereoisomer, nor does it exclude mixtures of isomers, tautomers, regioisomers or stereoisomers; however, it will be understood that a given isomer, tautomer, regioisomer or stereoisomer may have a higher level of activity than another isomer, tautomer, regioisomer or stereoisomer.
  • Compounds designed, selected and/or optimized by methods described above, once produced, can be characterized using a variety of assays known to those skilled in the art to determine whether the compounds have biological activity.
  • the molecules can be characterized by conventional assays, including but not limited to those assays described below, to determine whether they have a predicted activity, binding activity and/or binding specificity.
  • high-throughput screening can be used to speed up analysis using such assays.
  • it can be possible to rapidly screen the molecules described herein for activity, using techniques known in the art.
  • General methodologies for performing high-throughput screening are described, for example, in Devlin (1998) High Throughput Screening , Marcel Dekker; and U.S. Pat. No. 5,763,263.
  • High-throughput assays can use one or more different assay techniques including, but not limited to, those described below.
  • Step 1 Synthesis of methyl 5-(((trans)-4-((tert-butoxycarbonyl)amino)cyclohexyl)(ethyl)amino)-4′-hydroxy-4-methyl-[1,1′-biphenyl]-3-carboxylate
  • Step 2 Synthesis of methyl 5-(((trans)-4-((tert-butoxycarbonyl)amino)cyclohexyl) (ethyl)amino)-4′-(2-methoxyethoxy)-4-methyl-[1,1′-biphenyl]-3-carboxylate
  • Step 3 Synthesis of tert-butyl ((trans)-4-((5-(((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl) methyl) carbamoyl)-4′-(2-methoxyethoxy)-4-methyl-[1,1′-biphenyl]-3-yl(ethyl)-amino)-cyclohexyl) carbamate
  • Aqueous NaOH (0.066 g, 1.66 mmol in 5 mL H2O) was added to a solution of methyl 5-(((trans)-4-((tert-butoxycarbonyl)amino)cyclohexyl)(ethyl)amino)-4′-(2-methoxyethoxy)-4-methyl-[1,1′-biphenyl]-3-carboxylate (0.6 g, 1.11 mmol) in EtOH (10 mL) and stirred at 60° C. for 1 h. After completion of the reaction, ethanol was removed under reduced pressure and the residue was acidified using citric acid using to pH 4 was adjusted using citric acid. Extraction was carried out using 10% methanol in DCM. Combined organic layers were dried, concentrated giving respective acid (0.5 g, 85.6% yield).
  • Step 4 Synthesis of N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(((trans)-4-(dimethylamino)-cyclohexyl)(ethyl)-amino)-4′-(2-methoxyethoxy)-4-methyl-[1,1′-biphenyl]-3-carboxamide
  • Step 1 Synthesis of methyl 5-bromo-3-(((trans)-4-((tert-butoxycarbonyl)-(methyl)-amino)cyclohexyl)(ethyl)amino)-2-methylbenzoate
  • Step 2 Synthesis of methyl 3-(((trans)-4-((tert-butoxycarbonyl)-(methyl)amino)cyclohexyl)(ethyl)amino)-5-(3-hydroxyprop-1-yn-1-yl)-2-methylbenzoate
  • Step 3 Synthesis of methyl 5-(3-bromoprop-1-yn-1-yl)-3-(((trans)-4-((tert-butoxy carbonyl)(methyl)amino)cyclohexyl)(ethyl)amino)-2-methylbenzoate
  • Step 4 Synthesis of methyl 3-(((trans)-4-((tert-butoxycarbonyl)(methyl)amino)cyclohexyl)(ethyl)amino)-2-methyl-5-(3-morpholinoprop-1-yn-1-yl)benzoate
  • Step 5 Synthesis of tert-butyl ((trans)-4-(3-(((4,6-dimethyl-2-oxo-1,2-dihydro pyridin-3-yl)methyl)carbamoyl)-2-methyl-5-(3-morpholinoprop-1-yn-1-yl) phenyl)(ethyl)amino)cyclohexyl)(methyl)carbamate
  • Step 6 Synthesis of N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-3-(ethyl((trans)-4-(methylamino)cyclohexyl)amino)-2-methyl-5-(3-morpholinoprop-1-yn-1-yl)benzamide
  • Step 7 Synthesis of N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-3-(ethyl((trans)-4-((2-methoxyethyl)(methyl)amino)cyclohexyl)amino)-2-methyl-5-(3-morpholinoprop-1-yn-1-yl)benzamide
  • Step 1 Synthesis of methyl 5-bromo-3-(ethyl((trans)-4-(methylamino)cyclohexyl)amino)-2-methylbenzoate
  • Step 2 Synthesis of methyl 5-bromo-3-(ethyl((trans)-4-((2-methoxyethyl)(methyl)amino)cyclohexyl)amino)-2-methylbenzoate
  • Step 3 Synthesis of methyl 3-(ethyl((trans)-4-(2-methoxyethyl)(methyl)amino)cyclohexyl)amino)-2-methyl-5-(3-morpholinoprop-1-yn-1-yl)benzoate
  • the reaction mixture was heated at 105° C. for 4 h and then cooled to room temperature.
  • the reaction was quenched with water (100 mL) and the aqueous phase was extracted with 10% MeOH/DCM (400 mL ⁇ 3).
  • the combined organic extracts were dried over Na 2 SO 4 , filtered and concentrated.
  • the residue was, purified by silica gel column chromatography to afford the title compound (21 g, 63.7% yield).
  • Step 4 Synthesis of N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-3-(ethyl((trans)-4-((2-methoxyethyl)(methyl)amino)cyclohexyl)amino)-2-methyl-5-(3-morpholinoprop-1-yn-1-yl)benzamide
  • tetrakis(triphenylphosphine)palladium(0) (0.292 g, 0.253 mmol) was introduced and degassed for additional 10 min by bubbling nitrogen.
  • the reaction mixture was heated at 80° C. for 6 h.
  • the reaction was quenched with sat. NaHCO 3 , extracted with TBME (3 ⁇ 40 mL), dried over Na 2 SO 4 , filtered and concentrated.
  • the residue was purified by chromatography (0% to 40% AcOEt/Heptane) to give the titled compound (2.40 g, 98% yield).
  • the reaction mixture was directly concentrated and the residue was dissolved in DCM and then neutralized with sat. NaHCO 3 /brine.
  • the organic layer was dried (Na 2 SO 4 ) and filtered. And the filtrate was concentrated. The residue was used for alkylation without further purification (209 mg, 100%).
  • H3K27me0 (SEQ ID NO: 1) ATKAARKSAPATGGVKKPHRYRPGGK(biotin)-amide
  • H3K27me2 (SEQ ID NO: 2) ATKAARK(me2)SAPATGGVKKPHRYRPGGK(biotin)-amide
  • Chicken erythrocyte oligonucleosomes were purified from chicken blood according to established procedures.
  • PRC2 Complexes Human PRC2 complexes were purified as 4-component enzyme complexes co-expressed in Spodoptera frugiperda (sf9) cells using a baculovirus expression system. The subunits expressed were wild-type EZH2 (NM — 004456) or EZH2 Y641F, N, H, S or C mutants generated from the wild-type EZH2 construct, EED (NM — 003797), Suz12 (NM — 015355) and RbAp48 (NM — 005610). The EED subunit contained an N-terminal FLAG tag that was used to purify the entire 4-component complex from sf9 cell lysates.
  • the purity of the complexes met or exceeded 95% as determined by SDS-PAGE and Agilent Bioanalyzer analysis. Concentrations of enzyme stock concentrations (generally 0.3-1.0 mg/mL) was determined using a Bradford assay against a bovine serum albumin (BSA) standard.
  • BSA bovine serum albumin
  • DMSO DMSO (1 ⁇ L) was added to columns 11, 12, 23, 24, rows A-H for the maximum signal control, and SAH, a known product and inhibitor of PRC2 (1 ⁇ L) was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control.
  • a cocktail (40 ⁇ L) containing the wild-type PRC2 enzyme and H3K27me0 peptide or any of the Y641 mutant enzymes and H3K27me2 peptide was added by Multidrop Combi (Thermo). The compounds were allowed to incubate with PRC2 for 30 min at 25° C., then a cocktail (10 ⁇ L) containing a mixture of non-radioactive and 3 H-SAM was added to initiate the reaction (final volume 51 ⁇ L).
  • the final concentrations were as follows: wild-type or mutant PRC2 enzyme was 4 nM, SAH in the minimum signal control wells was 1 mM and the DMSO concentration was 1%. The final concentrations of the rest of the components are indicated in Table 2, below.
  • the assays were stopped by the addition of non-radioactive SAM (10 ⁇ L) to a final concentration of 600 ⁇ M, which dilutes the 3 H-SAM to a level where its incorporation into the peptide substrate is no longer detectable.
  • DMSO DMSO (1 ⁇ L) was added to columns 11, 12, 23, 24, rows A-H for the maximum signal control, and SAH, a known product and inhibitor of PRC2 (1 ⁇ L) was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control.
  • a cocktail (40 ⁇ L) containing the wild-type PRC2 enzyme and chicken erythrocyte oligonucleosome was added by Multidrop Combi (Thermo). The compounds were allowed to incubate with PRC2 for 30 min at 25° C., then a cocktail (10 ⁇ L) containing a mixture of non-radioactive and 3 H-SAM was added to initiate the reaction (final volume 51 ⁇ L).
  • the final concentrations were as follows: wild-type PRC2 enzyme was 4 nM, non-radioactive SAM was 430 nM, 3 H-SAM was 120 nM, chicken erythrocyte olumbleucleosome was 120 nM, SAH in the minimum signal control wells was 1 mM and the DMSO concentration was 1%.
  • the assay was stopped by the addition of non-radioactive SAM (10 ⁇ L) to a final concentration of 600 which dilutes the 3 H-SAM to a level where its incorporation into the chicken erythrocyte olignonucleosome substrate is no longer detectable.
  • top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit.
  • the Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit.
  • Y is the % inhibition and X is the compound concentration.
  • IC 50 values for the PRC2 enzyme assays on peptide substrates are presented in Table 3 below.
  • WSU-DLCL2 suspension cells were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany).
  • RPMI/Glutamax Medium, Penicillin-Streptomycin, Heat Inactivated Fetal Bovine Serum, and D-PBS were purchased from Life Technologies, Grand Island, N.Y., USA.
  • Extraction Buffer and Neutralization Buffer (5 ⁇ ) were purchased from Active Motif, Carlsbad, Calif., USA.
  • Rabbit anti-Histone H3 antibody was purchased from Abcam, Cambridge, Mass., USA.
  • Rabbit anti-H3K27me3 and HRP-conjugated anti-rabbit-IgG were purchased from Cell Signaling Technology, Danvers, Mass., USA.
  • TMB “Super Sensitive” substrate was sourced from BioFX Laboratories, Owings Mills, Md., USA.
  • IgG-free Bovine Serum Albumin was purchased from Jackson ImmunoResearch, West Grove, Pa., USA.
  • PBS with Tween (10 ⁇ PBST) was purchased from KPL, Gaithersburg, Md., USA.
  • Sulfuric Acid was purchased from Ricca Chemical, Arlington, Tex., USA.
  • Immulon ELISA plates were purchased from Thermo, Rochester, N.Y., USA.
  • V-bottom cell culture plates were purchased from Corning Inc., Corning, N.Y., USA.V-bottom polypropylene plates were purchased from Greiner Bio-One, Monroe, N.C., USA.
  • WSU-DLCL2 suspension cells were maintained in growth medium (RPMI 1640 supplemented with 10% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) and cultured at 37° C. under 5% CO 2 . Under assay conditions, cells were incubated in Assay Medium (RPMI 1640 supplemented with 20% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) at 37° C. under 5% CO 2 on a plate shaker.
  • growth medium RPMI 1640 supplemented with 10% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin
  • WSU-DLCL2 cells were seeded in assay medium at a concentration of 50,000 cells per mL to a 96-well V-bottom cell culture plate with 200 ⁇ L per well.
  • Compound (1 ⁇ L) from 96 well source plates was added directly to V-bottom cell plate. Plates were incubated on a titer-plate shaker at 37° C., 5% CO 2 for 96 hours. After four days of incubation, plates were spun at 241 ⁇ g for five minutes and medium was aspirated gently from each well of cell plate without disturbing cell pellet. Pellet was resuspended in 200 ⁇ L DPBS and plates were spun again at 241 ⁇ g for five minutes.
  • Histone H3 detection plate 100 ⁇ L per well were added of anti-Histone-H3 antibody (Abeam, ab1791) diluted 1:10,000 in ELISA Diluent.
  • H3K27 trimethylation detection plate 100 ⁇ L per well were added of anti-H3K27me3 diluted 1:2000 in ELISA diluent. Plates were incubated for 90 minutes at room temperature. Plates were washed three times with 300 ⁇ L 1 ⁇ PBST per well.
  • HRP-conjugated anti-rabbit IgG antibody diluted to 1:6000 in ELISA diluent was added per well.
  • H3K27me3 detection 100 ⁇ L of HRP conjugated anti-rabbit IgG antibody diluted to 1:4000 in ELISA diluent was added per well. Plates were incubated at room temperature for 90 minutes. Plates were washed four times with 1 ⁇ PBST 300 ⁇ L per well. TMB substrate 100 ⁇ L was added per well. Histone H3 plates were incubated for five minutes at room temperature. H3K27me3 plates were incubated for 10 minutes at room temperature. The reaction was stopped with sulfuric acid 1N (100 ⁇ L per well). Absorbance for each plate was read at 450 nm.
  • Each plate included eight control wells of DMSO only treatment (Minimum Inhibition) as well as eight control wells for maximum inhibition (Background wells).
  • Test compound was serially diluted three-fold in DMSO for a total of ten test concentrations, beginning at 25 ⁇ M. Percent inhibition was determined and IC 50 curves were generated using duplicate wells per concentration of compound. IC 50 values for this assay are presented in Table 3 below.
  • Percent ⁇ ⁇ Inhibition 100 - ( ( ( Individual ⁇ ⁇ Test ⁇ ⁇ Sample ⁇ ⁇ Ratio ) - ( Background ⁇ ⁇ Avg ⁇ ⁇ Ratio ) ( Minimum ⁇ ⁇ Inhibition ⁇ ⁇ Ratio ) - ( Background ⁇ ⁇ Average ⁇ ⁇ Ratio ) ) * 100 )
  • WSU-DLCL2 suspension cells were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany).
  • RPMI/Glutamax Medium, Penicillin-Streptomycin, Heat Inactivated Fetal Bovine Serum were purchased from Life Technologies, Grand Island, N.Y., USA.
  • V-bottom polypropylene 384-well plates were purchased from Greiner Bio-One, Monroe, N.C., USA.
  • Cell culture 384-well white opaque plates were purchased from Perkin Elmer, Waltham, Mass., USA.
  • Cell-Titer Glo® was purchased from Promega Corporation, Madison, Wis., USA.
  • SpectraMax M5 plate reader was purchased from Molecular Devices LLC, Sunnyvale, Calif., USA.
  • WSU-DLCL2 suspension cells were maintained in growth medium (RPMI 1640 supplemented with 10% v/v heat inactivated fetal bovine serum and cultured at 37° C. under 5% CO 2 . Under assay conditions, cells were incubated in Assay Medium (RPMI 1640 supplemented with 20% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) at 37° C. under 5% CO 2 .
  • N t N 0 ⁇ 2 t t D ( A ⁇ .1 )
  • N t is the cell number at a time point (t) after initiation of the observation period
  • N 0 is the cell number at the initiation of the observation period
  • t is the time after initiation of the observation period
  • t D is the time interval required for cell doubling, also referred to as the doubling time.
  • N t N 0 ⁇ e 0.693 ⁇ ⁇ t t D ( A ⁇ .2 )
  • the rate constant for cell proliferation (k p ) is inversely related to the doubling time as follows.
  • equation A.4 cell number is expected to increase exponentially with time during the early period of cell growth referred to as log-phase growth.
  • Changes in environmental conditions can result in a change in the rate of cellular proliferation that is quantifiable as changes in the proliferation rate constant k p .
  • an antiproliferative compound has an immediate impact on cell proliferation, one expects that plots of ln(N t ) as a function of time will continue to be linear at all compound concentrations, with diminishing values of k p at increasing concentrations of compound.
  • some compounds may not immediately effect a change in proliferation rate. Instead, there may be a period of latency before the impact of the compound is realized. In such cases a plot of ln(N t ) as a function of time will appear biphasic, and a time point at which the impact of the compound begins can be identified as the breakpoint between phases. Regardless of whether a compound's impact on proliferation is immediate or begins after a latency period, the rate constant for proliferation at each compound concentration is best defined by the slope of the ln(N t ) vs. time curve from the time point at which compound impact begins to the end of the observation period of the experiment.
  • the value of k p At compound concentrations for which the rate of cell growth exceeds that of cell killing, the value of k p will have a positive value (i.e., k p >0). At compound concentrations for which the rate of cell growth is less than that for cell killing, the value of k p will have a negative value (i.e., k p ⁇ 0) and the cell number will decrease with time, indicative of robust cytotoxicity.
  • k g exactly matches k d then the overall proliferation rate constant, k p , will have a value of zero.
  • LCC lowest cytotoxic concentration
  • the LCC represents a breakpoint or critical concentration above which frank cytotoxicity is observed, rather than a cytotoxic concentration per se.
  • the LCC can be viewed similar to other physical breakpoint metrics, such as the critical micelle concentration (CMC) used to define the concentration of lipid, detergent or other surfactant species above which all molecules incorporate into micellar structures.
  • CMC critical micelle concentration
  • the impact of antiproliferative compounds on cell growth has been most commonly quantified by the IC 50 value, which is defined as that concentration of compound that reduces the rate of cell proliferation to one half that observed in the absence of compound (i.e., for the vehicle or solvent control sample).
  • the IC 50 does not allow the investigator to differentiate between cytostatic and cytotoxic compounds.
  • the LCC in contrast, readily allows one to make such a differentiation and to further quantify the concentration at which the transition to robust cytotoxic behavior occurs.
  • k p ( k max - k min ) 1 + [ I ] I mid + k min ( A ⁇ .7 )
  • I mid is the concentration of compound yielding a value of k p that is midway between the values of k max and k min (note that the value of I mid is not the same as the IC 50 , except in the case of a complete and purely cytostatic compound).
  • fitting the replot data to equation A.7 provides estimates of k max , k min and I mid . If a compound is cytostatic (as defined here), the value of k min cannot be less than zero. For cytotoxic compounds, k min will be less than zero and the absolute value of k min will relate directly to the effectiveness of the compound in killing cells.
  • mice Female Fox Chase SCID® Mice (CB17/Icr-Prkdc scid /IcrIcoCrl, Charles River Laboratories) or athymic nude mice (Crl:NU(Ncr)-Foxn1 nu , Charles River Laboratories) were 8 weeks old and had a body-weight (BW) range of 16.0-21.1 g on Day 1 of the study.
  • the animals were fed ad libitum water (reverse osmosis 1 ppm CO and NIH 31 Modified and Irradiated Lab Diet® consisting of 18.0% crude protein, 5.0% crude fat, and 5.0% crude fiber.
  • mice were housed on irradiated Enrich-o'cobsTM bedding in static microisolators on a 12-hour light cycle at 20-22° C. (68-72° F.) and 40-60% humidity. All procedures complied with the recommendations of the Guide for Care and Use of Laboratory Animals with respect to restraint, husbandry, surgical procedures, feed and fluid regulation, and veterinary care.
  • Human lymphoma cell lines line were obtained from different sources (ATCC, DSMZ), e.g., Karpas-422 obtained from DSMZ.
  • the cell lines were maintained as suspension cultures in RPMI-1640 medium containing 100 units/mL penicillin G sodium salt, 100 g/mL streptomycin, 1% HEPES, and 1% L-Glutamine.
  • the medium was supplemented with 20% fetal bovine serum.
  • the cells were cultured in tissue culture flasks in a humidified incubator at 37° C., in an atmosphere of 5% CO 2 and 95% air.
  • Human lymphoma cell lines e.g., Karpas-422 cells
  • RPMI-1640 base media 50% MatrigelTM (BD Biosciences)
  • Each mouse received 1 ⁇ 10 7 cells (0.2 mL cell suspension) subcutaneously in the right flank. Tumors were calipered in two dimensions to monitor growth as the mean volume approached the desired 80-120 mm 3 range. Tumor size, in mm 3 , was calculated from:
  • Tumor weight can be estimated with the assumption that 1 mg is equivalent to 1 mm 3 of tumor volume. After 10-30 days mice with 145-150 mm 3 tumors were sorted into treatment groups with mean tumor volume of 147 mm 3 . Test Articles
  • Test compounds were stored at room temperature and protected from light. On each treatment day, fresh compound formulations were prepared by suspending the powders in 0.5% sodium carboxymethylcellulose (NaCMC) and 0.1% Tween ⁇ 80 in deionized water. The vehicle, 0.5% NaCMC and 0.1% Tween® 80 in deionized water, was used to treat the control groups at the same schedules. Formulations were stored away from light at 4° C. prior to administration. Unless otherwise specified, compounds referred to and tested in this experiment were in their specific salt forms mentioned in this paragraph.
  • NaCMC sodium carboxymethylcellulose
  • Tween® 80 0.1%
  • mice were treated at compound doses ranging from 62.5-500 mg/kg on a BID (2 times a day every 12 h) schedule for various amounts of days by oral gavage. Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals. The maximal treatment length was 28 days.
  • MTV Median Tumor Volume
  • TGI Tumor Growth Inhibition
  • MTV(n) the median tumor volume for the number of animals, n, evaluable on the last day, was determined for each group.
  • Percent tumor growth inhibition (% TGI) can be defined several ways. First, the difference between the MTV(n) of the designated control group and the MTV(n) of the drug-treated group is expressed as a percentage of the MTV(n) of the control group:
  • Another way of calculating % TGI is taking the change of the tumor size from day 1 to day n into account with n being the last treatment day.
  • mice were weighed daily on Days 1-5, and then twice weekly until the completion of the study. The mice were examined frequently for overt signs of any adverse, treatment related side effects, which were documented. Acceptable toxicity for the maximum tolerated dose (MTD) was defined as a group mean BW loss of less than 20% during the test, and not more than 10% mortality due to TR deaths. A death is to be classified as TR if it is attributable to treatment side effects as evidenced by clinical signs and/or necropsy, or due to unknown causes during the dosing period. A death is to be classified as NTR if there is evidence that the death is unrelated to treatment side effects.
  • MTD maximum tolerated dose
  • NTR deaths during the dosing interval would typically be categorized as NTRa (due to an accident or human error) or NTRm (due to necropsy-confirmed tumor dissemination by invasion and/or metastasis). Orally treated animals that die from unknown causes during the dosing period may be classified as NTRu when group performance does not support a TR classification and necropsy, to rule out a dosing error, is not feasible.
  • mice were sampled in a pre-specified fashion to assess target inhibition in tumors.
  • Tumors were harvested from specified mice under RNAse free conditions and bisected. Frozen tumor tissue from each animal was snap frozen in liquid N 2 and pulverized with a mortar and pestle.
  • tumor tissue was homogenized in 1.5 ml nuclear extraction buffer (10 mM Tris-HCl, 10 mM MgCl 2 , 25 mM KCl, 1% Triton X-100, 8.6% Sucrose, plus a Roche protease inhibitor tablet 1836145) and incubated on ice for 5 minutes. Nuclei were collected by centrifugation at 600 g for 5 minutes at 4° C. and washed once in PBS. Supernatant was removed and histones extracted for one hour, with vortexing every 15 minutes, with 0.4 N cold sulfuric acid. Extracts were clarified by centrifugation at 10000 g for 10 minutes at 4° C.
  • Histones were precipitated at ⁇ 20° C. for 2 hours-overnight, pelleted by centrifugation at 10000 g for 10 minutes, and resuspended in water.
  • Histones were prepared in equivalent concentrations in coating buffer (PBS+0.05% BSA) yielding 0.5 ng/uL of sample, and 100 uL of sample or standard was added in duplicate to 2 96-well ELISA plates (Thermo Labsystems, Immulon 4HBX #3885). The plates were sealed and incubated overnight at 4° C. The following day, plates were washed 3 ⁇ with 300 uL/well PBST (PBS+0.05% Tween 20; 10 ⁇ PBST, KPL #51-14-02) on a Bio Tek plate washer.
  • coating buffer PBS+0.05% BSA
  • Plates were blocked with 300 uL/well of diluent (PBS+2% BSA+0.05% Tween 20), incubated at RT for 2 hours, and washed 3 ⁇ with PBST. All antibodies were diluted in diluent. 100 uL/well of anti-H3K27me3 (CST #9733, 50% glycerol stock 1:1,000) or anti-total H3 (Abeam ab1791, 50% glycerol 1:10,000) was added to each plate. Plates were incubated for 90 min at RT and washed 3 ⁇ with PBST.
  • CST #9733 50% glycerol stock 1:1,000
  • anti-total H3 Abeam ab1791, 50% glycerol 1:10,000
  • Dosing Scheme Dose Dosing Group N Treatment (mg/kg) volume Route Schedule 1 5 Vehicle — 10 ⁇ l/g. p.o. BIDx7 2 5 Compound 1 62.5 10 ⁇ l/g p.o. BIDx7 3 5 Compound 1 83.3 10 ⁇ l/g p.o. BIDx7 4 5 Compound 1 125 10 ⁇ l/g p.o. BIDx7 5 5 Compound 1 166.7 10 ⁇ l/g p.o. BIDx7 6 5 Compound 1 250 10 ⁇ l/g p.o. BIDx7 7 5 Compound 1 333.3 10 ⁇ l/g p.o.
  • BIDx7 8 5 Compound 1 500 10 ⁇ l/g p.o. BIDx7 9 5 Compound A* 125 10 ⁇ l/g. p.o. BIDx7 10 5 Compound A 250 10 ⁇ l/g. p.o. BIDx7 *Compound A is N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(ethyl(tetrahydro-2H-pyran-4-yl)amino)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide.
  • Karpas-422 xenograft tumor bearing mice were treated with a compound at, e.g., 62.5, 125, 250, or 500 mg/kg BID for 28 days. There were 10 mice per group for the efficacy arm of the experiment. The tumor growth over the treatment course of 28 days for vehicle and test compound treated groups was measured.
  • Histones were extracted from tumors collected at the end of the study on day 28 for the efficacy cohort (3 h after the last dose for both cohorts). The H3K27me3 methyl mark was assessed for modulation with treatment in a dose dependent matter.
  • Dosing Scheme Dose Dosing Group N Treatment (mg/kg) volume Route Schedule 1 10 Vehicle — 10 ⁇ l/g. p.o. BIDx28 2 10 Compound 1 62.5 10 ⁇ l/g p.o. BIDx28 3 10 Compound 1 125 10 ⁇ l/g. p.o. BIDx28 4 10 Compound 1 250 10 ⁇ l/g. p.o. BIDx28 5 10 Compound 1 500 10 ⁇ l/g. p.o. BIDx28 6 10 Compound A* 250 10 ⁇ l/g. p.o.
  • BIDx28 *Compound A is N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(ethyl(tetrahydro-2H-pyran-4-yl)amino)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide.
  • TV was calculated from caliper measurements by the formula for the volume of a prolate ellipsoid (L ⁇ W 2 )/2 where L and W are the respective orthogonal length and width measurements (mm).
  • FIG. 3 is a diagram showing concentration of Compound 1 in tumor at day 7 or day 28 post treatment or concentration of Compound A in tumor at day 7 post treatment.
  • FIG. 4 is a diagram showing concentration of Compound 1 or Compound A in plasma at day 7 or day 28 post treatment.
  • the top dashed line indicates the plasma protein binding (PPB) corrected LCC of Compound A and the bottom dashed line indicates PPB corrected LCC of Compound 1.
  • FIG. 5 is a diagram showing global H3K27me3 methylation in KARPAS-422 tumors from mice treated with Compound 1 or Compound A for 7 days.
  • FIG. 6 is a diagram showing global H3K27me3 methylation in KARPAS-422 tumors from mice treated with Compound 1 for 28 days.
  • FIG. 7 is a diagram showing global H3K27me3 methylation in bone marrow from KARPAS-422 xenograft tumor bearing mice treated with Compound 1 or Compound A for 7 days.
  • FIG. 8 is a diagram showing global H3K27me3 methylation in bone marrow from KARPAS-422 xenograft tumor bearing mice treated with Compound 1 for 28 days.
  • A denotes vehicle treatment
  • B though “E” denote treatment with Compound 1 at dosages of 62.5, 125, 250, and 500 mg/kg, respectively
  • F denotes treatment with Compound A at a dosage of 250 mg/kg.
  • the metabolic stability of Compounds 1, 2, and 105 were evaluated in liver microsomes from five species, including mice, rats, dogs, monkeys, and humans.
  • the incubations were conducted in 96-well plates containing 250 ⁇ L total volume consisting of 100 mmol/L potassium phosphate buffer (pH 7.4), 1 mg/mL liver microsomes, test compound (i.e., Compounds 1, 2, or 105) at 8 concentrations, and 2 mg/mL NADPH.
  • concentrations of the compounds used for incubation ranged from 45.7 nM to 100 ⁇ M.
  • the addition of NADPH was used to start the reaction, and the incubations were done in a shaking water bath at 37° C. for up to 60 minutes. The reactions were terminated by adding an equal volume of stop solution containing Internal Standard (IS).
  • IS Internal Standard
  • the samples were then spun in a refrigerated centrifuge at 3000 RPM for a minimum of 5 minutes prior to analysis.
  • the LC/TOFMS systems were composed of a Shimadzu SIL-HTC autosampler (Kyoto, Japan), two pumps LC-20AD; Shimadzu Corp.), and a column oven (CTO-20AC; Shimadzu Corp.) with a time-of-flight mass spectrometer (AB SCIEX Qstar Elite, AB Sciex, Foster City, Calif.).
  • Peak areas of the test compound and IS for assay were integrated by Analyst QS (version 2.0, Applied Biosystems, Foster City, Calif.). Collision activated dissociation (CAD) with nitrogen was used to generate product ions. The optimized instrumental conditions were under positive ionization mode.
  • CAD Collision activated dissociation
  • the LC/MS/MS quantification was based on the ratios of peak areas of the test compound to that of the IS. Peak area calculation and integration of Compounds 1, 2, or 105 and IS utilized Analyst QS 2.0 (AB Sciex, Foster City, Calif.). Calculations were done using Excel (Office 2010, Microsoft Corp., Redmond, Wash.) and GraphPad Prism v. 5.02 (GraphPad Software Inc., La Jolla, Calif.). Data was analyzed and reported based on appropriate SOPs, such as those described in J. Lin, Pharmaceutical Research, 2006, 23(6):1089-1116; and Di L et al., Comb Chem High Throughput Screen. 2008 11(6):469-76.
  • Cl int ( ⁇ L/min/g liver) Cl int ( ⁇ L/min/mg microsomes) ⁇ Scaling Factor or Cl int ( ⁇ L/min/10 6 cells) ⁇ Scaling Factor.
  • the hepatocytes were obtained from BD Biosciences (Woburn, Mass.), and the appropriate media and DAPI nuclear stain were purchased from Life Technologies (Durham, N.C.).
  • Dulbecco's modified Eagle's Medium (DMEM), Dulbecco's phosphate buffered saline (DPBS), 100 ⁇ MEM non-essential amino acids, 100 ⁇ penicillin/streptomycin/glutamine solution, 2 ⁇ trypan blue were purchased from Mediatech (Manassas, Va.).
  • Fetal bovine serum (FBS) was acquired from Tissue Culture Biologicals (Tulare, Calif.).
  • the 24-well collagen coated plates for mRNA analysis were acquired from BD Biosciences (San Jose, Calif.).
  • Predesigned probes and primers were used in two triplex assays to assess change in mRNA.
  • the positive controls were ⁇ -naphthoflavone for CYP1A (1 and 10 ⁇ mmol/L), phenobarbital for CYP2B6 (100 ⁇ mol/L and 1 mmol/L), and rifampicin for CYP2C9 and CYP3A (1 and 10 ⁇ mol/L).
  • DMSO was used as the vehicle (negative) control.
  • CYP form specific assays were performed after the treatment period, and cells were counted to determine viability.
  • the cryopreserved hepatocytes were thawed in a 37° C. water bath and plated according to vendor instructions.
  • One tube of hepatocytes was added to a 50 mL conical tube containing Life Technologies cryopreserved hepatocyte recovery medium (CHRM).
  • CHRM Life Technologies cryopreserved hepatocyte recovery medium
  • the cells were spun in a Beckman centrifuge with a GH 3.8 rotor at 800 RPM for 10 minutes. The supernatant was removed and the cells were resuspended in plating media for counting. After counting, the cells were resuspended at 0.75 million viable cells/mL.
  • the suspension (0.5 mL/well) was added into a 24-well collagen coated plate, or, after the addition of 60 ⁇ L of DMEM containing 10% FBS, penicillin/streptomycin/glutamine, and MEM non-essential amino acids, 80 ⁇ L of the suspension was added to each well of a 96-well collagen coated plate. After swirling and rocking to provide better plate coverage, the cells were placed in a tissue culture incubator at 5% CO 2 and 37° C. and allowed to attach overnight. The cells were then treated using CellzDirect hepatocyte maintenance media. The cells were exposed to Compound 1, 2, or 105 (1 or 10 ⁇ mol/L) or vehicle for 48 hours. During the treatment, the maintenance media and test compounds were replenished every 24 hours.
  • the cells were washed with DPBS. After washing with DPBS, the cells were fixed using 3.7% p-formaldehyde in DPBS for one hour. The formaldehyde was removed and 0.6 ⁇ mol/L DAPI in DPBS was added. The cells were stained by DAPI for 20 minutes and then washed three times with DPBS. Cells were counted using an ArrayScan II (Cellomics, Pittsburgh, Pa.) with a 5 ⁇ objective lens. Fraction of hepatocytes remaining was calculated using the number of cells found at a treatment condition divided by cells found with the vehicle control.
  • the mRNA concentration was measured via a Nanodrop ND-1000 (Wilmington, Del.). The mRNA concentration was normalized for every sample within a donor.
  • the reverse transcription was performed with a Superscript VILO cDNA synthesis kit from Life Technologies following manufacturer's directions. After cDNA synthesis, quantitative real time PCR was performed using a 7500 Fast Real Time PCR system from Applied Biosystems, a wholly owned subsidiary of Life Technologies.
  • the reaction components for real time PCR consisted of: 10 ⁇ L of Taqman Fast Advanced Master Mix (Life Technologies), 2 ⁇ L cDNA, 5 ⁇ L nuclease free water (Life Technologies), 1 ⁇ L of primer limited FAM labeled assay 14500984230 ml for 13-2 microglobulin, 1 ⁇ L of primer limited VIC labeled assay HS00167927_m1 for CYP1A2 or HS04183483_g1 for CYP2B6, and 1 ⁇ L of primer limited NED labeled assay HS04260376_m1 for CYP2C9 or HS00604506_ml for CYP3A4. Calculations of fold difference as compared to vehicle control were done by 7500 Software version 2.0.5 (Life Technologies) using the ⁇ C t method. Calculations of E max and EC 50 were done using GraphPad Prism.
  • Compound 1 exhibited no significant induction (except potentially CYP2C9); Compound 2 exhibited no induction (with slightly lower activity); and Compound 105 exhibited induction of CYP2B6, CYP2C9, and CYP3A. No significant loss of cell viability was observed.
  • CYP cytochromes P450
  • the competitive inhibition potential of Compounds 1, 2, and 105 was determined by assessing at multiple concentrations on probe CYP reactions near their respective K m values to create IC 50 curves in human liver microsomes (HLM).
  • the time-dependent inactivation (TDI) potential was also assessed for CYP3A4/5 by evaluating K I and k inact values when appropriate.
  • a suspension containing PB, HLM, CYP-selective probe substrate, and the inhibitor being tested was added to a 96-well plate.
  • the plates were preincubated in a 37° C. water bath for approximately 2 minutes.
  • the reaction was initiated by the addition of NADPH to each well of the 96-well plate.
  • the final concentrations for PB, HLM, and NADPH were 100 mmol/L (pH 7.4), 0.1 mg/mL, and 2.3 mmol/L, respectively.
  • the CYP probe substrates and CYP inhibitors used as positive controls and their respective concentrations are listed below. The final MeOH concentration used in each incubation did not exceed 0.8%.
  • a suspension containing PB, HLM, and the inhibitor stocks was added to a 96-well plate.
  • the plates were preincubated in a 37° C. water bath for approximately 2 minutes.
  • the reaction was initiated by the addition of NADPH to each well of the 96-well plate and carried out for 0, 5, 10, 15, 20, and 30 minutes.
  • PB solution was substituted for NADPH stock solution.
  • the final concentrations for PB, HLM, and NADPH were 100 mmol/L (pH 7.4), 0.2 mg/mL, and 2.3 mmol/L, respectively.
  • the HPLC system used was a Shimadzu HPLC system (Kyoto, Japan) consisting of a SIL-HTC autosampler, a DGU-14A degasser, three LC-10ADvp pumps, and a CTO-10ACvp column oven.
  • the samples were analyzed on an API4000QTrap (AB Sciex, Foster City, Calif.) triple quadrupole mass spectrometer using turbo spray ionization under positive ion mode.

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